Macromolecular MS Project Summary The importance of the structure-function relationship of proteins and protein-complexes motivates the direct measurement of protein structure in the gas phase by mass spectrometry. This method, termed native mass spectrometry or native electrospray ionization, allows the study of intact complexes and the determination of stoichiometry. The native proteins and complexes can also be investigated by a variety of activation methods to determine structural information. These methods include collisionally activated dissociation (CAD), electron capture/transfer dissociation (ECD/ETD), and infrared multi- photon dissociation (IRMPD). Among the systems we will interrogate using these methods are: (1) Lipoprotein complexes, such as high-density lipoproteins (HDLs) whose heterogeneity is of interest. HDL is an important indicator of cardiovascular health. (2) Membrane-embedded proteins play key roles in cell biology and are pharmaceutical targets (e.g., in anesthesia). (3) Proteins with flexible regions are often actively involved in function and interfacing to other proteins. (4) The stoichiometry of very large protein assemblies is among the first information needed to understand system function and it is still very difficult to get for large complexes. (5) Crosslinking studies provide distance constraints and aid in modeling the geometries of large complexes.